I think there are two sides of illness information to record.
The first side is your input/output. That is, the stuff that affects you and the results your body gets. I keep a log of all the factors and symptoms I think may be relevant. Example factors: what I eat, what supplements I take, whether I get particularly stressed. Example symptoms: sore joints, grogginess waking, sore skin, bowel movements.
Many of these things I record as they happen. For the rest I have a list of things I note daily measurements of.
You can't really begin to understand how a particular supplement or therapy effects you unless you keep track of your symptoms and test the therapy at least a couple times. "I took taurine and I got a headache." Yeah? How much taurine? When did you take it? What else did you eat? Oh, and did you consider that you also banged your head on the cabinet that day? And did you notice that your anxiety went down a couple days later?
I didn't adopt this "record all signs, check each therapy at least twice to be sure" perspective until a couple years into my investigation. There were some things I'd looked into early on that I wish I'd stayed with, but I didn't clearly see their benefit at the time.
Okay, the second side of illness information is your research into biology, nutrition, pharmacokinetics, syndromes, etc. (Low sodium causes dehydration. Low aldosterone causes low sodium. High cortisol can cause cortisol shunt. Cortisol shunt hogs hormone building blocks so you don't build as much aldosterone. The mucus lining of the gut is critical. The mucus lining is built up by so-and-so nutrients, and it takes so much time to build up. High copper levels end up stored in brain and liver. Symptoms of high copper are... Etc. etc.) Frankly, I do a poor job of tracking this information.
Whenever I see something interesting I take a note on the idea in a file. "High cortisol is related to reduced glutathione levels." And I write down the URL where I got the information. "http://www.detoxwithmax.com/health-conditions/chronic-fatigue-and-glutathione/". That's it. It's better than nothing. I can search the file for terms related to things I'm thinking about or researching.
But it can be hard to be motivated enough to summarize a finding, so I often end up just storing links. But you can't search the notes file for the bit that was interesting if you don't note it in the file. And I'm sick and tired of all the research and nose grinding, so am I going to want to re-read web pages I've been to, just because I have links?
I imagine an ideal system where you study stuff, write up summaries of important stuff and store the links/references, and make flashcards of the really important facts. Trying to memorize stuff while suffering "Adrenal Fatigue" is not easy, so doing it without concerted effort will just have the process drag on. I often vaguely recall, "Oh, hell, I knew something about this nutrient that was critical in just this situation..."
"Mind mapping" might be the thing to do. I know some flashcard programs, perhaps SuperMemo, include a mode where you can take notes and then build flashcards from notes. That sounds great.
Having a mystery illness and trying to help yourself get out of it is like being a student at school, where your academic performance magically affects your health.